These reports about bone density issues in bicyclists have been floating around for many years. My understanding is that there are 2 flaws in most of these reports:
1. They always compare bicycling to other sports like running. Other studies show that any type of exercise, including bicycling, is better for your bones than no exercise at all.
2. Some of the reports are about ultra endurance cyclists (who ride 400 miles/week or more). Data for those types of bicyclists may or may not have any relevance to your typical 100 mile/week recreational cyclist.
Not applicable to many of us, I'd say. Also, competitive racers probably aren't doing any cross-training. 1-2 deadlift (or squats, or kettle-bell, or any other full-body load-bearing exercises) would prevent bone loss.
Anyway, when your upper body begins to look like that of a wet cat, you should be worried about bone loss.